Tandem mass spectrometry methods (MS/MS) are very useful for characterizing and/or quantifying a component of interest in a complex mixture and/or for deriving enhanced structural information from an analyte that yields limited fragmentation and/or has a feature that complicates quantification. Linear ion traps are one type of instrumentation commonly used for MS/MS. The term “linear ion trap” may include three dimensional ion traps (e.g. 3-D ion traps) made up of ring and end-cap electrodes forming a near ideal quadrupole field or ion traps comprising four pole rods (e.g., 2-D ion traps). In an ideal 3-D ion trap quadrupole field, a radio frequency (RF) field strength increases linearly both radially and axially and the repulsing pseudo-forces also increase linearly. The 2-D ion traps are made up of four rod electrodes in which the quadrupole field only changes along two coordinates (x, y) and remains constant along the third coordinate (z).
Typically, 3-D ion traps have a small octopole field in addition to the quadrupole field. The octopole component makes the 3-D ion trap a substantially non-linear resonating system (A. A. Makarov, Anal. Chem. 1996, 68, p. 4257-4263, Franzen, et al., Practical aspects of Ion Trap Mass Spectrometry, volume 1 p. 69 edited by R. E. March and J.F.J. Todd). This means that isolation is asymmetrical both below the m/z of interest and above it. With a positive sign of the octopole field the isolation window can be very sharp for m/z below the nominal m/z value and quite diffused above the nominal m/z value.
Isolation techniques such as those described in U.S. Pat. No. 5,324,939 do not recognize the non-linearity of the ion trap and focus on the construction of the ejection waveforms based on the assumption of a linear resonance system. As a result the isolation procedure requires a substantial amount of time (i.e., on the order of 20 to 60 ms) and the width of the isolation window is typically greater than 1 Da.
Franzen in U.S. Pat. No. 5,331,157 (the '157 Patent) recognized the non-linear behavior and non-symmetrical ion behavior around the m/z of interest and disclosed the use of a non-linear resonance to facilitate the ejection of M+1 species from an ion trap. However when using the technique of the '157 Patent, it is typically difficult to obtain an isolation window width better then 1Da. Further the ejection of ions with masses higher than the m/z of interest typically requires repeating the procedure. When using the technique of the '157 Patent, it is desirable to have a lower number of ions stored in the ion trap. Thus, typically the total number of ions that can be stored in the ion trap prior to isolation (e.g., the “isolation storage capacity”) is limited.
U.S. Pat. No. 6,649,911 discloses a complex specially designed wave function used, with phase inversion at around the frequency that corresponds to the mass to be isolated, for trapping ions. Repeating application of the scan function is typically necessary to provide isolation of a well resolved ion species.
Superimposing a substantial contribution of an octopole field onto the pure quadrupole field of a 2-D ion trap has been suggested recently. (See Linear Quadrupoles with Added Octopole Fields, Sudakov at the Proceedings of the 51 ASMS, Canada, Jun. 8-12, 1993; and Franzen, U.S. Patent Publication U.S. 2004/0051036 A1). However, adding an octopole component in a 2-D ion trap utilizing prior art isolation methods typically results in a diffused isolation edge on the one side of the isolation window.
Accordingly, there is a need for isolation apparatus and methods for a 2-D ion trap with a superimposed octopole field.